Hi all,
This is a two-pronged change proposal - first to allow BioJava to make correct
use of the bioentry_dbxref tables in BioSQL, and second to allow it to parse
reference information correctly from EMBL, Genbank, Genpept, GenXML, and
SwissProt records and store them within Sequence objects in a consistent manner.
Currently, references are loaded from only some of the above formats. Depending
on the format, they are stored in different ways within Sequence object.
Genbank references are stored with each line of the record as a separate
annotation. eg. one annotation with a key saying REFERENCE and value giving a
location, another with a key saying AUTHOR and a value listing them, etc. etc.
As simple String/String annotations, they get persisted to the
bioentry_qualifer_value table in BioSQL. As multiple references are read, they
get stored with the same keys, so you end up with Annotations for these keys
containing ArrayLists of potentially different arity, depending on which of the
original references had which optional fields included (eg. PUBMED or MEDLINE).
This makes it impossible to accurately reconstruct the original reference
information when exporting the sequence to a file.
EMBL/Swissprot references do almost the same thing, except the parser here
gathers up the various reference tags from the file and wraps each set in its
own ReferenceAnnotation class, which is just a map which gets flattened out and
persisted to bioentry_qualifier_value as String/String annotation pairs as
above. When loaded back in from BioSQL the ReferenceAnnotation objects are not
recreated, and you end up with the same ArrayList problem as above, leading to
the same problem when trying to export the sequence to a file.
Another problem here is that the two approaches only understand their own
methods when it comes to exporting references in their own file formats. So,
the Genbank exporter cannot export references that were loaded from
EMBL/Swissprot, and vice versa.
Not good!
So, I propose the following:
1) Change the file format parsers above to create, when reading
sequences from file, an org.biojava.bibliography.BibRef objects for each
inputted reference. This object can then be stored against the Sequence as an
annotation, with the key of BibRef.class. As with all other kinds of
annotation, if multiple references are loaded then the value of the annotation
should be an ArrayList of the various BibRef objects. If only one reference is
loaded, then the value should be the single BibRef object itself.
2) Change the file format parsers above to understand, when writing
sequences to file, how to convert BibRef annotations into their own formats.
3) There is no restriction on which of the established BibRef subtypes
from org.biojava.bibliography.* you can actually use to annotate the sequence.
Usually you'll be wanting a BiblioJournalArticle object. However, you MUST use
certain fields as follows:
a) use the 'identifier' field to store the PubMed or MedLine ID
(purely the ID, not prefixed with anything).
b) use the 'publisher' field to store a BiblioOrganisation
object with name set to 'PUBMED' or 'MEDLINE' as appropriate (must be upper
case - if not, it will get changed to upper case on persistence to BioSQL, so
you might as well stick it in upper case to start with).
c) use the 'type' field to store a TYPE_* value from
BibRefSupport to indicate what sort of resource this reference refers to (in
most cases you'll want TYPE_JOURNAL_ARTICLE).
4) To alter BioSQLSequenceDB.persistBioentryProperty() to check for
annotations with the key of BibRef.class or any of its established subtypes as
above, and use special behaviour to persist these to the bioentry_dbxref table
(and related tables as appropriate).
5) To alter BioSQLSequenceAnnotation.initAnnotations() to check for and
load the bioentry_dbxref data as BibRef.class annotations.
Any suggestions/changes/volunteers/violent objections? I can manage steps 4 and
5 myself quite easily, but will need help from everyone out there in updating
the file parsers to use this proposed mechanism.
cheers,
Richard
Richard Holland
Bioinformatics Specialist
Genome Institute of Singapore
60 Biopolis Street, #02-01 Genome, Singapore 138672
Tel: (65) 6478 8000 DID: (65) 6478 8199
Email: [EMAIL PROTECTED]
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